Don't label outside of layer's bbox

CHANGELOG.unreleased.md

@@ -24,6 +24,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Fixed
 - Fixed that layer bounding boxes were sometimes colored green even though this should only happen for tasks. [#8535](https://github.com/scalableminds/webknossos/pull/8535)
 - Fixed that annotations could not be opened anymore (caused by #8535). [#8599](https://github.com/scalableminds/webknossos/pull/8599)
+- Voxels outside of the layer bounding box cannot be brushed, anymore. [#8602](https://github.com/scalableminds/webknossos/pull/8602)
 
 ### Removed
 

frontend/javascripts/libs/utils.ts

@@ -15,7 +15,10 @@ import type { BoundingBoxObject, NumberLike } from "oxalis/store";
 import type { APIDataset, APIUser } from "types/api_types";
 import type { ArbitraryObject, Comparator } from "types/globals";
 
+export type Writeable<T> = { -readonly [P in keyof T]: T[P] };
+
 type UrlParams = Record<string, string>;
+
 // Fix JS modulo bug
 // http://javascript.about.com/od/problemsolving/a/modulobug.htm
 export function mod(x: number, n: number) {

frontend/javascripts/oxalis/api/api_latest.ts

@@ -13,14 +13,15 @@ import type { ToastStyle } from "libs/toast";
 import Toast from "libs/toast";
 import UserLocalStorage from "libs/user_local_storage";
 import * as Utils from "libs/utils";
-import { coalesce } from "libs/utils";
+import { type Writeable, coalesce, mod } from "libs/utils";
 import window, { location } from "libs/window";
 import _ from "lodash";
 import messages from "messages";
 import type {
   BoundingBoxType,
   BucketAddress,
   ControlMode,
+  LabeledVoxelsMap,
   OrthoView,
   TypedArray,
   Vector3,
@@ -69,6 +70,7 @@ import {
 } from "oxalis/model/accessors/skeletontracing_accessor";
 import { AnnotationTool, type AnnotationToolId } from "oxalis/model/accessors/tool_accessor";
 import {
+  enforceActiveVolumeTracing,
   getActiveCellId,
   getActiveSegmentationTracing,
   getNameOfRequestedOrVisibleSegmentationLayer,
@@ -131,6 +133,7 @@ import {
   type BatchableUpdateSegmentAction,
   batchUpdateGroupsAndSegmentsAction,
   clickSegmentAction,
+  finishAnnotationStrokeAction,
   removeSegmentAction,
   setActiveCellAction,
   setSegmentGroupsAction,
@@ -139,6 +142,7 @@ import {
 import BoundingBox from "oxalis/model/bucket_data_handling/bounding_box";
 import type { Bucket, DataBucket } from "oxalis/model/bucket_data_handling/bucket";
 import type DataLayer from "oxalis/model/data_layer";
+import Dimensions from "oxalis/model/dimensions";
 import dimensions from "oxalis/model/dimensions";
 import { MagInfo } from "oxalis/model/helpers/mag_info";
 import { parseNml } from "oxalis/model/helpers/nml_helpers";
@@ -148,10 +152,13 @@ import {
   globalPositionToBucketPosition,
   scaleGlobalPositionWithMagnification,
   zoomedAddressToZoomedPosition,
+  zoomedPositionToZoomedAddress,
 } from "oxalis/model/helpers/position_converter";
 import { getConstructorForElementClass } from "oxalis/model/helpers/typed_buffer";
 import { getMaximumGroupId } from "oxalis/model/reducers/skeletontracing_reducer_helpers";
 import { getHalfViewportExtentsInUnitFromState } from "oxalis/model/sagas/saga_selectors";
+import { applyLabeledVoxelMapToAllMissingMags } from "oxalis/model/sagas/volume/helpers";
+import { applyVoxelMap } from "oxalis/model/volumetracing/volume_annotation_sampling";
 import { Model, api } from "oxalis/singletons";
 import type {
   DatasetConfiguration,
@@ -412,7 +419,8 @@ class TracingApi {
    * @example
    * const comment = api.tracing.getCommentForNode(23);
    *
-   * @example // Provide a tree for lookup speed boost
+   * @example
+   * // Provide a tree for lookup speed boost
    * const comment = api.tracing.getCommentForNode(23, api.getActiveTreeid());
    */
   getCommentForNode(nodeId: number, treeId?: number): string | null | undefined {
@@ -1814,14 +1822,17 @@ class DataApi {
    * If the zoom level is provided and points to a not existent mag,
    * 0 will be returned.
    *
-   * @example // Return the greyscale value for a bucket
+   * @example
+   * // Return the greyscale value for a bucket
    * const position = [123, 123, 123];
    * api.data.getDataValue("binary", position).then((greyscaleColor) => ...);
    *
-   * @example // Using the await keyword instead of the promise syntax
+   * @example
+   * // Using the await keyword instead of the promise syntax
    * const greyscaleColor = await api.data.getDataValue("binary", position);
    *
-   * @example // Get the segmentation id for the first volume tracing layer
+   * @example
+   * // Get the segmentation id for the first volume tracing layer
    * const segmentId = await api.data.getDataValue(api.data.getVolumeTracingLayerIds()[0], position);
    */
   async getDataValue(
@@ -1995,7 +2006,7 @@ class DataApi {
       bucketPositionToGlobalAddress(bucketAddress, new MagInfo(magnifications));
 
     const nextBucketInDim = (bucket: BucketAddress, dim: 0 | 1 | 2) => {
-      const copy = bucket.slice() as BucketAddress;
+      const copy = bucket.slice() as Writeable<BucketAddress>;
       copy[dim]++;
       return copy;
     };
@@ -2120,7 +2131,8 @@ class DataApi {
    * Downloads a cuboid of raw data from a dataset (not tracing) layer. A new window is opened for the download -
    * if that is not the case, please check your pop-up blocker.
    *
-   * @example // Download a cuboid (from (0, 0, 0) to (100, 200, 100)) of raw data from the "segmentation" layer.
+   * @example
+   * // Download a cuboid (from (0, 0, 0) to (100, 200, 100)) of raw data from the "segmentation" layer.
    * api.data.downloadRawDataCuboid("segmentation", [0,0,0], [100,200,100]);
    */
   downloadRawDataCuboid(layerName: string, topLeft: Vector3, bottomRight: Vector3): Promise<void> {
@@ -2156,32 +2168,115 @@ class DataApi {
   }
 
   /**
-   * Label voxels with the supplied value. Note that this method does not mutate
-   * the data immediately, but instead returns a promise (since the data might
-   * have to be downloaded first).
+   * Label voxels with the supplied value. This method behaves as if the user
+   * had brushed the provided voxels all at once. If the volume data wasn't
+   * downloaded completely yet, WEBKNOSSOS will merge the data as soon as it
+   * was downloaded.
    *
    * _Volume tracing only!_
    *
-   * @example // Set the segmentation id for some voxels to 1337
-   * await api.data.labelVoxels([[1,1,1], [1,2,1], [2,1,1], [2,2,1]], 1337);
+   * @example
+   * // Set the segmentation id for some voxels to 1337
+   * api.data.labelVoxels([[1,1,1], [1,2,1], [2,1,1], [2,2,1]], 1337);
    */
-  async labelVoxels(
-    voxels: Array<Vector3>,
+  labelVoxels(
+    globalPositionsMag1: Vector3[],
     label: number,
-    additionalCoordinates: AdditionalCoordinate[] | null = null,
-  ): Promise<void> {
-    assertVolume(Store.getState());
-    const segmentationLayer = this.model.getEnforcedSegmentationTracingLayer();
-    await Promise.all(
-      voxels.map((voxel) =>
-        segmentationLayer.cube._labelVoxelInAllResolutions_DEPRECATED(
-          voxel,
+    optAdditionalCoordinates?: AdditionalCoordinate[] | null,
+  ) {
+    const state = Store.getState();
+    const allowUpdate = state.annotation.restrictions.allowUpdate;
+    const additionalCoordinates =
+      optAdditionalCoordinates === undefined
+        ? state.flycam.additionalCoordinates
+        : optAdditionalCoordinates;
+    if (!allowUpdate || globalPositionsMag1.length === 0) return;
+
+    const volumeTracing = enforceActiveVolumeTracing(state);
+    const segmentationLayer = Model.getSegmentationTracingLayer(volumeTracing.tracingId);
+    const { cube } = segmentationLayer;
+    const magInfo = getMagInfo(segmentationLayer.mags);
+    const labeledZoomStep = magInfo.getClosestExistingIndex(0);
+    const labeledMag = magInfo.getMagByIndexOrThrow(labeledZoomStep);
+    const dimensionIndices = Dimensions.getIndices(OrthoViews.PLANE_XY);
+    const thirdDim = dimensionIndices[2];
+
+    const globalPositions = globalPositionsMag1.map(
+      (pos): Vector3 => [
+        Math.floor(pos[0] / labeledMag[0]),
+        Math.floor(pos[1] / labeledMag[1]),
+        Math.floor(pos[2] / labeledMag[2]),
+      ],
+    );
+    const groupedByW = _.groupBy(globalPositions, (pos) => pos[thirdDim]);
+
+    for (const [wValueStr, group] of Object.entries(groupedByW)) {
+      const w = Number.parseInt(wValueStr, 10);
+      const currentLabeledVoxelMap: LabeledVoxelsMap = new Map();
+
+      for (const pos of group) {
+        const bucketZoomedAddress = zoomedPositionToZoomedAddress(
+          pos,
+          labeledZoomStep,
           additionalCoordinates,
-          label,
-        ),
+        );
+
+        let labelMap = currentLabeledVoxelMap.get(bucketZoomedAddress);
+        if (!labelMap) {
+          labelMap = new Uint8Array(Constants.BUCKET_WIDTH ** 2);
+          currentLabeledVoxelMap.set(bucketZoomedAddress, labelMap);
+        }
+
+        const a = pos[dimensionIndices[0]];
+        const b = pos[dimensionIndices[1]];
+        const localA = mod(a, Constants.BUCKET_WIDTH);
+        const localB = mod(b, Constants.BUCKET_WIDTH);
+        labelMap[localA * Constants.BUCKET_WIDTH + localB] = 1;
+      }
+
+      const numberOfSlices = 1;
+      applyVoxelMap(
+        currentLabeledVoxelMap,
+        cube,
+        label,
+        (x, y, out) => {
+          out[0] = x;
+          out[1] = y;
+          out[2] = w;
+        },
+        numberOfSlices,
+        thirdDim,
+        true,
+        0,
+      );
+
+      const thirdDimensionOfSlice = w * labeledMag[thirdDim];
+
+      applyLabeledVoxelMapToAllMissingMags(
+        currentLabeledVoxelMap,
+        labeledZoomStep,
+        dimensionIndices,
+        magInfo,
+        cube,
+        label,
+        thirdDimensionOfSlice,
+        true,
+        0,
+      );
+    }
+
+    Store.dispatch(
+      updateSegmentAction(
+        label,
+        {
+          somePosition: globalPositionsMag1[0],
+          someAdditionalCoordinates: additionalCoordinates || undefined,
+        },
+        volumeTracing.tracingId,
       ),
     );
-    segmentationLayer.cube.pushQueue.push();
+
+    Store.dispatch(finishAnnotationStrokeAction(volumeTracing.tracingId));
   }
 
   /**
@@ -2741,7 +2836,8 @@ class UtilsApi {
   /**
    * Wait for some milliseconds before continuing the control flow.
    *
-   * @example // Wait for 5 seconds
+   * @example
+   * // Wait for 5 seconds
    * await api.utils.sleep(5000);
    */
   sleep(milliseconds: number): Promise<void> {
@@ -2756,7 +2852,8 @@ class UtilsApi {
    * @param {string} type - Can be one of the following: "info", "warning", "success" or "error"
    * @param {string} message - The message string you want to show
    * @param {number} timeout - Time period in milliseconds after which the toast will be hidden. Time is measured as soon as the user moves the mouse. A value of 0 means that the toast will only hide by clicking on it's X button.
-   * @example // Show a toast for 5 seconds
+   * @example
+   * // Show a toast for 5 seconds
    * const removeToast = api.utils.showToast("info", "You just got toasted", false, 5000);
    * // ... optionally:
    * // removeToast();

frontend/javascripts/oxalis/api/wk_dev.ts

@@ -4,7 +4,7 @@ import { V3 } from "libs/mjs";
 import { roundTo, sleep } from "libs/utils";
 import _ from "lodash";
 import { type OrthoView, OrthoViews, type Vector3 } from "oxalis/constants";
-import { Store } from "oxalis/singletons";
+import { Model, Store } from "oxalis/singletons";
 import type { ApiInterface } from "./api_latest";
 import type ApiLoader from "./api_loader";
 
@@ -59,6 +59,11 @@ export default class WkDev {
     return Store;
   }
 
+  public get model() {
+    /* Access to the model */
+    return Model;
+  }
+
   public get api() {
     /* Access to the API (will fail if API is not initialized yet). */
     if (this._api == null) {

frontend/javascripts/oxalis/constants.ts

@@ -20,8 +20,8 @@ export type NestedMatrix4 = [Vector4, Vector4, Vector4, Vector4]; // Represents
 // For 3D data BucketAddress = x, y, z, mag
 // For higher dimensional data, BucketAddress = x, y, z, mag, [{name: "t", value: t}, ...]
 export type BucketAddress =
-  | Vector4
-  | [number, number, number, number, AdditionalCoordinate[] | null];
+  | readonly [number, number, number, number]
+  | readonly [number, number, number, number, AdditionalCoordinate[] | null];
 
 export type Point2 = {
   x: number;
@@ -49,11 +49,11 @@ export type Rect = {
   height: number;
 };
 export const AnnotationContentTypes = ["skeleton", "volume", "hybrid"];
-export const Vector2Indicies = [0, 1];
-export const Vector3Indicies = [0, 1, 2];
-export const Vector4Indicies = [0, 1, 2, 3];
-export const Vector5Indicies = [0, 1, 2, 3, 4];
-export const Vector6Indicies = [0, 1, 2, 3, 4, 5];
+export const Vector2Indicies = [0, 1] as const;
+export const Vector3Indicies = [0, 1, 2] as const;
+export const Vector4Indicies = [0, 1, 2, 3] as const;
+export const Vector5Indicies = [0, 1, 2, 3, 4] as const;
+export const Vector6Indicies = [0, 1, 2, 3, 4, 5] as const;
 export enum OrthoViews {
   PLANE_XY = "PLANE_XY",
   PLANE_YZ = "PLANE_YZ",